The objective of this research is to develop a new generation of ultra-high-throughput screening (uHTS) systems based on surface-enhanced Raman scattering (SERS) detection. The specific aims of the project are: Aim 1. Develop a multi-spectral Raman system (MRS) as the optical readout for uHTS. Aim 2: Evaluate the uHTS-MRS using molecular sentinels for highly parallel ligand/target binding detection. Aim 3: Develop and integrate an automated system for detection of optical signals from SERS-based nanoprobes. Aim 4: Evaluate the CMOS-uHTS system for high throughput screening of small molecules or mRNA probes in a cellular model. Our system will offer a new dimension in label multiplexing for characterizing large numbers of samples in cell-based high-throughput screening for drug discovery. A novel SERS-based molecular-sentinel detection scheme will be applied for multiplex gene expression analysis. The unique features of the proposed system include: Novel instrumentation based on multi-spectral imaging detection Novel detection scheme based on combination of molecular recognition and SERS detection The SERS effect enhances the sensitivity of conventional Raman signal over 106-1015 fold SERS-MS nanoprobes are insensitive to photo-bleaching (often associated with fluorescent probes). Ultra high-throughput "label multiplex" detection (i.e. capability for many Raman dye-labeled probes to be used simultaneously) (the extremely narrow Raman bands allow SERS to be used as a multiplexing technique). The system will be tested for screening of small molecules, synthetic chemical and natural product libraries that up- or down-regulate expression of various families of mRNA. Active compounds that are capable of modulating mRNA gene expression levels will be identified, followed by additional assays. The SERS-based uHTS instrumentation will provide a tool that has the potential to be faster and more efficient than currently available systems, and is capable to provide great sensitivity with higher levels of specificity, and multiplexing capabilities to screen synthetic chemical and natural product libraries such as the ones that will be registered and housed in the NIH-sponsored molecular libraries screening centers.